Contacts of the helix formed by residues 120 - 129 (chain B) in PDB entry 1H9T
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B ALA 3.7 2.9 - - - +
119B GLN* 1.3 103.5 + - + +
121B PRO* 1.3 74.5 - - - +
122B ASP* 3.0 12.7 + - - +
123B LYS* 2.8 24.5 + - + +
124B ALA 2.9 9.5 + - - -
155B ALA* 3.3 24.2 - - - +
157B GLY* 4.1 18.3 - - - -
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Residues in contact with PRO 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA 4.1 4.7 - - - +
117B PHE* 3.1 23.7 - - - +
118B ARG 4.5 4.0 - - - +
119B GLN* 3.5 2.0 - - - -
120B HIS* 1.3 93.3 - - - +
122B ASP* 1.3 76.5 + - + +
124B ALA* 3.2 12.6 + - + +
125B GLN* 3.3 7.8 + - - +
200B CYS* 3.4 18.7 - - - +
1231B AU 3.9 18.2 - - - -
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B HIS* 3.6 9.1 + - - +
121B PRO* 1.3 98.6 - - + +
123B LYS* 1.3 61.2 + - - +
125B GLN* 3.3 21.8 - - - +
126B GLU* 3.7 5.2 + - - +
200B CYS* 5.3 0.2 - - - -
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLY 5.0 0.4 + - - -
239A ARG* 3.1 49.6 + - + +
120B HIS* 2.8 18.5 + - + +
122B ASP* 1.3 76.7 - - - +
124B ALA* 1.3 57.4 + - - +
125B GLN 2.6 14.7 + - - -
126B GLU* 3.2 26.5 + - + +
127B VAL* 3.1 24.6 - - + +
151B GLY* 4.8 11.3 + - - -
154B PHE* 5.1 2.0 - - - +
155B ALA* 4.0 18.6 - - + +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA* 3.6 33.0 - - + +
117B PHE* 4.9 11.2 - - + -
120B HIS 2.9 5.3 + - - -
121B PRO* 3.2 12.7 + - + +
123B LYS* 1.3 77.4 - - - +
125B GLN* 1.3 62.4 + - - +
127B VAL* 4.2 5.4 - - - -
128B LEU* 2.8 33.7 + - + +
152B LEU* 4.9 5.6 - - + -
155B ALA* 4.5 7.0 - - + +
200B CYS* 5.1 5.4 - - + -
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B PRO 3.3 3.8 + - - +
122B ASP* 3.3 13.7 - - - +
123B LYS 2.6 1.4 - - - -
124B ALA* 1.3 81.3 - - - +
126B GLU* 1.3 55.2 + - - +
127B VAL 2.6 16.8 + - - -
128B LEU* 3.0 3.7 + - - +
129B ALA* 2.9 24.1 + - - +
197B SER* 3.3 37.7 + - - +
200B CYS* 2.9 46.3 - - - +
201B SER* 4.0 9.5 + - - +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ASP 3.7 6.9 + - - +
123B LYS* 3.2 27.0 + - + +
125B GLN* 1.3 76.5 - - - +
127B VAL* 1.3 57.3 + - + +
129B ALA* 3.8 11.1 - - + +
130B THR* 3.2 21.7 + - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LYS* 3.1 33.9 - - + +
124B ALA* 3.9 3.1 - - - +
125B GLN 2.6 5.7 + - - -
126B GLU* 1.3 73.8 - - - +
128B LEU* 1.3 62.3 + - + +
129B ALA 2.8 4.3 - - - -
130B THR* 2.3 47.8 + - + +
147B ASN 4.5 1.3 - - - +
148B ILE* 3.8 26.4 - - + +
151B GLY* 4.2 22.7 - - - +
152B LEU* 3.7 19.1 - - + -
155B ALA* 5.0 0.9 - - + -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B PHE* 6.4 1.8 - - + -
124B ALA* 2.8 23.6 - - + +
125B GLN* 3.0 3.7 + - - +
127B VAL* 1.3 74.5 - - + +
129B ALA* 1.3 61.4 + - - +
131B ALA* 3.2 19.8 - - - +
132B ASN* 5.1 1.4 + - - +
148B ILE* 4.1 18.4 - - + -
152B LEU* 3.3 28.7 - - + -
193B TYR* 3.8 39.5 - - + +
194B HIS* 5.8 0.5 + - - -
196B LEU* 4.5 13.9 - - + -
197B SER* 4.0 33.5 + - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLN 2.9 16.8 + - - +
126B GLU* 3.8 12.8 - - + +
127B VAL 2.8 0.6 + - - -
128B LEU* 1.3 75.0 - - - +
130B THR* 1.3 54.1 + - - +
131B ALA 2.5 17.8 + - - -
132B ASN* 2.9 31.2 + - - +
133B GLU* 4.6 2.1 + - - +
197B SER* 5.2 1.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il